Taxonomy and the tree of life

This right here is a picture of Carl Linnaeus, and I'm sure I'm mispronouncing the word. He's a Swedish gentleman who lived in the 1700s, and he's known as the father of modern taxonomy. And the word taxonomy, if you just split up into its original root, it really is the science of really classifying things. But when people talk about taxonomy-- and in particular, in Carl Linnaeus' case-- they're talking about the classification of living things, so classifying organisms. And his real innovation-- before he came about, peopled realize that you had species of animals, that lions had certain properties that made them all lions, that they could interbreed and things like that, that monkey or chimpanzees would all interbreed and that would be a separate species and that polar bears were separate species and that humans were a separate species. But what he really brought to the table was he decided, well, let me not just group animals into species. Maybe I can group species into other categories. And that's where we get the genus from. You group similar species into a genus. And then he went even beyond that, because even the idea of grouping things into a genus dated back to the ancient Greeks. He said, well, why don't I group similar genuses together into orders, orders together into classes, and then classes together into kingdoms. So really what he did is he said, well, maybe I can classify-- I can create a tree. I can create a tree of life. I can create a structure so we can really see how far apart any two organisms are, and so that's why he's really the father about modern taxonomy. And he did not have many tools. All he could do was look at his powers of observations and say, OK, those kind of animals, they have fur, or they reproduce in this way. Or they lay eggs, or they don't lay eggs. Or they have spinal columns, or they don't have spinal columns. So that's the best that he could do when he did his taxonomy. But since then, there's obviously been tons of innovations in how we perceive animals, or the natural world, and our tools for studying them. So one thing that he did not know about is evolution-- this idea of common ancestry. And between our understandings of evolution and our ability to look back at the fossil record, that helps us get more precise at figuring out which animals are related to which. We can see, do they have a common ancestor more recent or further back. And what even Charles Darwin didn't have, which we now use as a tool in taxonomy, is the genetic evidence. So now we don't even have to rely on the fossil record. We could look at the DNA of two species that exist today and see how similar is that DNA. And that tells us how recently they branched apart if we were able to find it in the fossil record or how recently in the past did these two species become two different species. Now, with that said, I do want to make this clear. And this is something that I've always had a little bit-- it was fuzzy for me the first time that I was exposed to this idea of taxonomy-- is that taxonomy is as much an art as it's a science. And today, even to this day, people are debating about the best way to classify things and what do you pay attention to. And DNA has been the best tool so far in giving us a more systematic, a more analytical way, of deciding how close two animals are. But to a large degree, a lot of these categories-- deciding where to divide along kingdom, phylum, class, order, family, tribe-- these are somewhat arbitrary. These are just picked based on early taxonomists, including Carl Linnaeus, and saying, well, this looks like a grouping right over here. But they could have grouped at a broader level or a deeper level. So these things right over here are somewhat arbitrary. A more analytical way is just to see how much DNA you have in common and then use that as a measure of how far apart two animals are. Or really, I should say, two species are, because this taxonomy doesn't only apply just to animals. It applies to plants and bacteria and Archaea and all sorts of things, so it's actually a broader thing than just animals. Now, with that out of the way, what I thought would be fun-- just so that we could really get a sense of where modern taxonomy is, where the field that was essentially fathered by Carl Linnaeus, where it is now, how we-- and use that to figure out where we humans fit into the big picture. And obviously, I'm drawing just a small fraction of the universe of the organisms that we even know about right now. But at least it frames the picture in terms of something we understand-- in particular, us. In particular, humans. Now, our species, we call ourselves humans. But we're really Homo sapiens. And the sapiens is the species part, and then Homo is the genus. And what I'm doing right over here is I'm saying, well, if Homo is the genus, what other species were inside of Homo? And the reality is-- or at least as far as we know-- there are no other living species inside of Homo. We probably killed them all off. Or maybe we interbreeded with them somehow, which might have argued that maybe they weren't different species. But more likely, they were competing in the same ecosystems, and they became endangered species very quickly when they competed with our ancestors. But the most recent other species within the genus that we know about are the neanderthals, and the formal term for their species is neanderthalensis. Now, if we go further up the tree of life, further up the taxonomy-- and you'll sometimes see tribe mentioned. Sometimes you won't. And we tend to get a little bit more granular the closer we get to humans. When we go further away in the tree of life, we get a little bit less granular sometimes. But that's not always the case as well. You go a little bit further up, then you get Hominini. And I'm sure I'm mispronouncing some of this as well. But another species that's in Homonini that is not in Homo-- and I'm definitely not listing all of them, and that's why I'm showing all of these other branches over here-- is what we call the common chimpanzee. And their species name is-- their genus is Pan, and their species is troglodytes. So you would refer to them as Pan troglodytes. And that's also another convention that Carl Linnaeus came up with, is that you refer to a particular species by its genus and then its species. And you capitalize the genus, and you lowercase a species. So we're Homo sapiens. This is Homo neanderthalensis. This Pan troglodytes or often referred to as chimpanzees. Now, if you go up one higher level of broadness on this tree of life, you then get to the family. And we are in the family Hominidae, and I'm sure I'm mispronouncing it once again. But just to give you an example, so everything I've listed so far, everything I've talked about so far are within this family. And to show you an animal that is not in this family, you just have to look at the gorilla. And you could call it the Gorillini gorilla, or G gorilla. That's its actual species name. And this family right over here, sometimes the common term is the great apes. Now, you go one further level-- and the whole reason why I'm doing this-- and I'm not by any means being exhaustive about the other species that are in that family, but that are not in our tribe. I'm just trying to give you a picture of-- as we get further and further out, as we get further out of our tribe, our family, our order, we're getting to things where the common ancestry with human goes further and further back in time. The genetic similarities become more and more different. And even just the physical differences, if we look it at a very superficial level, become more and more and more different. So you get to even a broader category. This is where you get to the primates, and this is probably something that you might be somewhat familiar with. And the term primates is generally these animals that look like they either live in trees or a rain forest, or they're a descendant of things that live in trees. So they have these things that they can grasp things with. They're good at climbing, broadly. Not all of them are. Humans are probably the worst primates when it comes to climbing, or one of the worst. But that's the general classification. That's what we generally think of when we think of primates. And if we think of a primate that is not a great ape, you just have to think of a baboon. So this right here is a baboon. It is a primate, but it is not a great ape. It is probably a descendant-- some baboons actually don't live in trees. But all of them are probably a descendant from things that first lived in trees, and that's why their hands and their feet look the way they do. Now you get to even a broader level of classification. You get to the mammals. And once again, probably something you're used to thinking about. Mammals are air-breathing animals, and they tend to have fur or hair. They tend to provide some form of milk for their young. They have active mammary glands. There's other things we can talk about, what makes a mammal. I'm not going to go into the rigorous definition. But just to give you an example of a mammal that is not a primate, I could show you this polar bear right over here. This is a mammal that is not a primate. And I could do other things. I could show you a tiger, or I could show you a giraffe or a horse. And so by no stretch of the imagination am I being comprehensive. But let's keep getting broader. Now let's go to the class-- we're already at the class of Mammalia. Now let's go to the phylum. In phylum, we are-- humans and all mammals, we are in the phylum chordates. And chordates, we're actually in the subphylum, which I didn't write here, vertebrates, which means we have a vertebra. We have a spinal column with a spinal cord in it. Chordates are a little bit more general. Chordates is a phylum where-- kind of the arrangement of where the mouth is, where are the digestive organs, where the anus is, where the spinal column is, where are the brains, where are the eyes, where are the mouth. They're kind of all in the same place. And if you think about it, everything I've listed here kind of has the same general structure. You have a spinal column. You have a brain. You have a mouth. Then the mouth leads to some type digestive column. And at the end of it, you have an anus over there. And you have eyes in front of the brain. And so this is a general way-- and I'm not being very rigorous here, is how you describe a chordate. And to show a chordate that is not a mammal, you would just have to think of a fish or sharks. So this right over here is a non-mammal chordate This is a great white shark over here. Now, let's go even broader. As you'll see, now we're going to things that are very, very not human-like. So you go one step broader. Now we're in Animalia, the kingdom of animals. And this is the broadest category that Carl Linnaeus thought about. Well actually, he did go into trees as well. But when you think of kingdom animals and you think of things that aren't chordates, you start going into things like insects. And you start going into things like jellyfish. If you go even broader, now we're talking about the domain. You go to Eukarya. So these are all organisms that have cells. And inside those cells, they have complex structures. So if you're a Eukarya, you have cells with complex structures. If you're a Prokarya, you don't have complex structures inside your cell. But other Eukarya that are not animals include things like plants. And obviously, I'm giving no justice to this whole branch of the tree of life. It could be just as rich or richer than everything I've drawn over here. This is just a small fraction of the entire tree of life, but let's go even broader than that. So if you go even broader than that, you say, well, what's a kind of life form that isn't Eukarya, that wouldn't have these more complex cell structures, the mitochondria in the cells, the cell nucleuses? Then you just have to think about something like bacteria. And if you want to go even broader, there's things like viruses that you could even debate whether they really even are life, because they are dependent on other life forms for their actual reproduction. But they do have genetic material, like everything else. And that, to me, is kind of a mind-blowing idea. As different as a plant is-- look at a house plant that is in your house right now or the tree when you walk home or bacteria or this jellyfish. There is a commonality in that we all have DNA. And that DNA, for the most part, replicates in a very, very, very, similar way. So it's actually crazy that we actually even are related or that we even do have a common ancestor with some of these things. And then it even begs the question, well, what about things like viruses? Anyway, I'll leave you here. And I really just want to let you know that-- make sure you realize that this is a-- it's definitely worth studying, because we understand where we fit in in the universe of living things. But I also want to let you know that it is a little bit of an art on where you decide where to make these classifications or where you decide to focus on, whether you want to focus on what properties, whether it's how they reproduce or how they feed their young or can they move around or what they breathe or whatever, things like that. Anyway, I'll let you go there.